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- PDB-3syx: Crystal Structure of the WH1 domain from human sprouty-related, E... -

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Basic information

Entry
Database: PDB / ID: 3syx
TitleCrystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.
ComponentsSprouty-related, EVH1 domain-containing protein 1
KeywordsSIGNALING PROTEIN / WH1 domain / Human sprouty-related / EVH1 domain-containing protein / Q7Z699 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / PSI-Biology
Function / homology
Function and homology information


regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of epithelial to mesenchymal transition / negative regulation of cell migration involved in sprouting angiogenesis / protein serine/threonine kinase inhibitor activity / negative regulation of MAPK cascade ...regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of epithelial to mesenchymal transition / negative regulation of cell migration involved in sprouting angiogenesis / protein serine/threonine kinase inhibitor activity / negative regulation of MAPK cascade / negative regulation of peptidyl-threonine phosphorylation / regulation of MAPK cascade / RAS signaling downstream of NF1 loss-of-function variants / phosphatase binding / negative regulation of angiogenesis / caveola / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / Regulation of RAS by GAPs / protein kinase binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
YTTRIUM (III) ION / Sprouty-related, EVH1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.453 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sprouty-related, EVH1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9192
Polymers14,8301
Non-polymers891
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.754, 52.754, 121.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-201-

YT3

Detailsmonomer,18.07 kD,95.2%

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Components

#1: Protein Sprouty-related, EVH1 domain-containing protein 1 / Spred-1 / hSpred1


Mass: 14829.955 Da / Num. of mol.: 1 / Fragment: WH1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRED1 / Plasmid: pET 14-15C, HR5538B-13-131-14.6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q7Z699
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 6
Details: 12% PEG 20000, 0.1 M potassium acetate, 10 mM yttrium(III) chloride, 0.1 M MES, pH 6.0, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97896 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97896 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 27822 / Num. obs: 27739 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 55.94 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.6
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2826 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XOD

1xod


Resolution: 2.453→26.377 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 27.8 / Stereochemistry target values: ML
Details: There is a yttrium atom located in special position with occupancy 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 650 4.7 %RANDOM
Rwork0.228 ---
obs0.23 13821 99.54 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.482 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 147.9 Å2 / Biso mean: 63.317 Å2 / Biso min: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.896 Å2-0 Å2-0 Å2
2--3.896 Å2-0 Å2
3----7.791 Å2
Refinement stepCycle: LAST / Resolution: 2.453→26.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 1 21 955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009953
X-RAY DIFFRACTIONf_angle_d1.6641280
X-RAY DIFFRACTIONf_chiral_restr0.12136
X-RAY DIFFRACTIONf_plane_restr0.006165
X-RAY DIFFRACTIONf_dihedral_angle_d16.719355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.453-2.6420.4351170.3726812798100
2.642-2.9080.41490.3126052754100
2.908-3.3280.3671400.23726412781100
3.328-4.190.251320.2282568270098
4.19-26.3780.1941120.18926762788100

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